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Protein

Cytolethal distending toxin subunit B

Gene

cdtB

Organism
Escherichia coli
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Part of the tripartite complex that is required for the CDT activity. CdtB exhibits a DNA-nicking endonuclease activity, and very probably causes DNA damage in intoxicated cells. This damage induces G2/M cell cycle arrest, chromatin fragmentation, cell distention and nucleus enlargement.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Toxin

Protein family/group databases

TCDBi1.C.98.1.1. the cytolethal distending toxin (cdt) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytolethal distending toxin subunit B
Short name:
CDT B
Alternative name(s):
Deoxyribonuclease CdtB (EC:3.1.-.-)
Gene namesi
Name:cdtB
OrganismiEscherichia coli
Taxonomic identifieri562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia

Subcellular locationi

  • Secreted 1 Publication

  • Note: Localized to the nucleus of the infected cells.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi154H → A: When the mutant protein is introduced in HeLa cells, it does not result in cell cycle arrest. Devoid of DNA-nicking/DNase activity. 2 Publications1
Mutagenesisi229D → A: Loss of DNase activity, no cellular distension, no G2/M cell cycle arrest. 1 Publication1
Mutagenesisi260D → R: Loss of DNase activity, no cellular distension, no G2/M cell cycle arrest. 1 Publication1
Mutagenesisi261H → A: Loss of DNase activity, no cellular distension, no G2/M cell cycle arrest. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 18Sequence analysisAdd BLAST18
ChainiPRO_000001337319 – 269Cytolethal distending toxin subunit BAdd BLAST251

Interactioni

Subunit structurei

Heterotrimer of 3 subunits, CdtA, CdtB and CdtC.

Structurei

Secondary structure

1269
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi20 – 22Combined sources3
Beta strandi25 – 32Combined sources8
Helixi38 – 42Combined sources5
Helixi44 – 49Combined sources6
Beta strandi56 – 63Combined sources8
Beta strandi85 – 90Combined sources6
Beta strandi93 – 97Combined sources5
Beta strandi99 – 105Combined sources7
Beta strandi109 – 111Combined sources3
Beta strandi116 – 122Combined sources7
Beta strandi125 – 130Combined sources6
Beta strandi140 – 145Combined sources6
Beta strandi148 – 154Combined sources7
Beta strandi157 – 160Combined sources4
Helixi163 – 175Combined sources13
Helixi180 – 183Combined sources4
Beta strandi186 – 192Combined sources7
Helixi197 – 201Combined sources5
Helixi206 – 210Combined sources5
Beta strandi212 – 215Combined sources4
Beta strandi229 – 237Combined sources9
Beta strandi245 – 248Combined sources4
Turni249 – 252Combined sources4
Beta strandi264 – 267Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2F1NX-ray1.73A19-269[»]
ProteinModelPortaliQ46669.
SMRiQ46669.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46669.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi195 – 210Nuclear localization signalAdd BLAST16

Keywords - Domaini

Signal

Family and domain databases

CDDicd09081. CdtB. 1 hit.
Gene3Di3.60.10.10. 1 hit.
InterProiIPR003539. CD_toxinB.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PfamiPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
PIRSFiPIRSF018539. CDT_B. 1 hit.
PRINTSiPR01388. CDTOXINB.
SUPFAMiSSF56219. SSF56219. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q46669-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKYIISLIV FLSFYAQADL TDFRVATWNL QGASATTESK WNINVRQLIS
60 70 80 90 100
GENAVDILAV QEAGSPPSTA VDTGTLIPSP GIPVRELIWN LSTNSRPQQV
110 120 130 140 150
YIYFSAVDAL GGRVNLALVS NRRADEVFVL SPVRQGGRPL LGIRIGNDAF
160 170 180 190 200
FTAHAIAMRN NDAPALVEEV YNFFRDSRDP VHQALNWMIL GDFNREPADL
210 220 230 240 250
EMNLTVPVRR ASEIISPAAA TQTSQRTLDY AVAGNSVAFR PSPLQAGIVY
260
GARRTQISSD HFPVGVSRR
Length:269
Mass (Da):29,529
Last modified:November 1, 1996 - v1
Checksum:i958B09BD6C73EBB5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U04208 Unassigned DNA. Translation: AAA18786.1.
PIRiI69095.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U04208 Unassigned DNA. Translation: AAA18786.1.
PIRiI69095.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2F1NX-ray1.73A19-269[»]
ProteinModelPortaliQ46669.
SMRiQ46669.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

TCDBi1.C.98.1.1. the cytolethal distending toxin (cdt) family.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiQ46669.

Family and domain databases

CDDicd09081. CdtB. 1 hit.
Gene3Di3.60.10.10. 1 hit.
InterProiIPR003539. CD_toxinB.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PfamiPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
PIRSFiPIRSF018539. CDT_B. 1 hit.
PRINTSiPR01388. CDTOXINB.
SUPFAMiSSF56219. SSF56219. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCDTB_ECOLX
AccessioniPrimary (citable) accession number: Q46669
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 66 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The operon of the strain O128:H- / 9142-88 / EPEC is referred to as cdt type II (CDT-II).

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.